[R] How can I avoid a for-loop through sapply or lapply ?

[Steve Lianoglou]

Hi,

On Sep 29, 2009, at 12:03 PM, <mauede at alice.it> wrote:

> Through converting a miRNAs file from FASTA to character  format I  
> get a vector which looks like the following:
>
>> nml
>  [1] "hsa-let-7a MIMAT0000062 Homo sapiens let-7a"
>  [2] "hsa-let-7b MIMAT0000063 Homo sapiens let-7b"
>  [3] "hsa-let-7c MIMAT0000064 Homo sapiens let-7c"
>  [4] "hsa-let-7d MIMAT0000065 Homo sapiens let-7d"
>  [5] "hsa-let-7e MIMAT0000066 Homo sapiens let-7e"
>  [6] "hsa-let-7f MIMAT0000067 Homo sapiens let-7f"
>  [7] "hsa-miR-15a MIMAT0000068 Homo sapiens miR-15a"
>  [8] "hsa-miR-16 MIMAT0000069 Homo sapiens miR-16"
>  [9] "hsa-miR-17 MIMAT0000070 Homo sapiens miR-17"
> [10] "hsa-miR-18a MIMAT0000072 Homo sapiens miR-18a"
>        .......................................................................................................
> [888] "hsa-miR-675* MIMAT0006790 Homo sapiens miR-675*"
> [889] "hsa-miR-888* MIMAT0004917 Homo sapiens miR-888*"
> [890] "hsa-miR-541* MIMAT0004919 Homo sapiens miR-541*"
>
>
> My goal is to separate into a vector only the first string preceding  
> the 1st space starting from the left.
> With reference to the records above listed I would obtain:
> [1] "hsa-let-7a"
>  [2] "hsa-let-7b"
>  [3] "hsa-let-7c"
>  [4] "hsa-let-7d"
>  [5] "hsa-let-7e"
>  [6] "hsa-let-7f f"
>  [7] "hsa-miR-15a"
>  [8] "hsa-miR-16"
>  [9] "hsa-miR-17"
> [10] "hsa-miR-18a"
>        .......................................................................................................
> [888] "hsa-miR-675*"
> [889] "hsa-miR-888*"
> [890] "hsa-miR-541*"

pieces <- strsplit(nml, " ")
sapply(pieces, '[', 1)

Or, the same as a 1 liner:
sapply(strsplit(nml, " "), '[', 1)

Hope that helps,

-steve

--
Steve Lianoglou
Graduate Student: Computational Systems Biology
   |  Memorial Sloan-Kettering Cancer Center
   |  Weill Medical College of Cornell University
Contact Info: http://cbio.mskcc.org/~lianos/contact